I am using 6.5 Home edition. I closed the application and restarted and it is saving changes this far. If problem happens again, I will post more information
I really think you should upgrade to the latest version, as besides all enhancements and new features, it also comes with numerous bug fixes. Some of these bugs can lead to incorrect fonts, which can indeed be very annoying.
People who upgrade in May will also get a free upgrade to FontCreator version 9 (which will be released within a couple of weeks), so what are you waiting for
FontCreator 6.5 is not that old yet — it is not even four years yet since it was released, and the next version 7 was only released in June 2013. Anyone using the Home Edition may be using it only occasionally, so $50 for an upgrade may not be justifiable for everyone.
However, if you do decide to upgrade, many improvements have been made in the last three versions, and many more again will follow in version 9. Take a look at my review page for the key changes to date.
Pros: Improved interface, group-based kerning, automatic hinting, colour font support, OpenType feature support, Web Open Font Format export, CFF outlines export, project files save settings for each font project.
Cons: It will take some effort to get up to speed with the newer versions.